PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2P8U
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (162 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN 3-HYDROXY-3-METHYLGLUTARYL COA SYNTHASE I
Authors
:
A. Turnbull, N. Shafqat, E. Salah, F. H. Niesen, N. Burgess, G. Bunkoczi J. Debreczeni, A. C. W. Pike, C. Umeano, F. Gorrec, F. Von Delft, J. Wei C. H. Arrowsmith, M. Sundstrom, A. Edwards, U. Oppermann, Structural Consortium (Sgc)
Date
:
23 Mar 07 (Deposition) - 03 Apr 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydromethylglutaryl Coa, Mevalonate Pathway, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. Shafqat, A. Turnbull, J. Zschocke, U. Oppermann, W. W. Yue
Crystal Structures Of Human Hmg-Coa Synthase Isoforms Provide Insights Into Inherited Ketogenesis Disorders And Inhibitor Design.
J. Mol. Biol. V. 398 497 2010
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: COENZYME A (COAa)
1b: COENZYME A (COAb)
2a: GLYCEROL (GOLa)
3a: S-ACETYL-CYSTEINE (SCYa)
3b: S-ACETYL-CYSTEINE (SCYb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
COA
2
Ligand/Ion
COENZYME A
2
GOL
1
Ligand/Ion
GLYCEROL
3
SCY
2
Mod. Amino Acid
S-ACETYL-CYSTEINE
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:43 , ALA A:44 , GLY A:45 , LYS A:46 , GLY A:50 , TYR A:163 , ASN A:167 , ALA A:168 , THR A:171 , SER A:221 , PRO A:266 , TYR A:267 , LYS A:269 , LEU A:270 , LYS A:273 , HOH A:1097 , HOH A:1252
BINDING SITE FOR RESIDUE COA A 601
2
AC2
SOFTWARE
LYS A:461 , ARG A:463 , LYS B:461 , ARG B:463 , HOH B:795
BINDING SITE FOR RESIDUE GOL A 981
3
AC3
SOFTWARE
ALA B:44 , GLY B:45 , LYS B:46 , GLY B:50 , TYR B:163 , ASN B:167 , ALA B:168 , THR B:171 , SER B:221 , PRO B:266 , TYR B:267 , LYS B:269 , LEU B:270 , LYS B:273 , HOH B:638 , HOH B:698 , HOH B:774 , HOH B:776 , HOH B:819 , HOH B:866 , HOH B:895 , HOH B:909 , HOH B:912 , HOH B:936 , HOH B:966
BINDING SITE FOR RESIDUE COA B 601
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: HMG_COA_SYNTHASE (A:117-132,B:117-132)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
HMG_COA_SYNTHASE
PS01226
Hydroxymethylglutaryl-coenzyme A synthase active site.
HMCS1_HUMAN
117-132
2
A:117-132
B:117-132
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.4b (A:9-150 (gaps) | B:9-150 (gaps))
Exon 1.5 (A:150-192 | B:150-192)
Exon 1.6 (A:192-247 | B:192-247)
Exon 1.7a (A:247-302 | B:247-302)
Exon 1.8a (A:302-359 | B:302-359)
Exon 1.9a (A:359-395 | B:359-395)
Exon 1.10 (A:395-437 | B:395-437)
Exon 1.11 (A:437-470 | B:437-470)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.3/1.4b
2: Boundary 1.4b/1.5
3: Boundary 1.5/1.6
4: Boundary 1.6/1.7a
5: Boundary 1.7a/1.8a
6: Boundary 1.8a/1.9a
7: Boundary 1.9a/1.10
8: Boundary 1.10/1.11
9: Boundary 1.11/1.12
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000325110
1b
ENSE00001383321
chr5:
43313595-43313458
138
HMCS1_HUMAN
-
0
0
-
-
1.3
ENST00000325110
3
ENSE00001558269
chr5:
43307926-43307868
59
HMCS1_HUMAN
-
0
0
-
-
1.4b
ENST00000325110
4b
ENSE00001267132
chr5:
43299077-43298620
458
HMCS1_HUMAN
1-150
150
2
A:9-150 (gaps)
B:9-150 (gaps)
147
147
1.5
ENST00000325110
5
ENSE00000971122
chr5:
43298236-43298111
126
HMCS1_HUMAN
150-192
43
2
A:150-192
B:150-192
43
43
1.6
ENST00000325110
6
ENSE00000821231
chr5:
43297268-43297104
165
HMCS1_HUMAN
192-247
56
2
A:192-247
B:192-247
56
56
1.7a
ENST00000325110
7a
ENSE00001175150
chr5:
43296019-43295854
166
HMCS1_HUMAN
247-302
56
2
A:247-302
B:247-302
56
56
1.8a
ENST00000325110
8a
ENSE00000742609
chr5:
43294963-43294793
171
HMCS1_HUMAN
302-359
58
2
A:302-359
B:302-359
58
58
1.9a
ENST00000325110
9a
ENSE00000742607
chr5:
43294264-43294158
107
HMCS1_HUMAN
359-395
37
2
A:359-395
B:359-395
37
37
1.10
ENST00000325110
10
ENSE00000742605
chr5:
43293075-43292950
126
HMCS1_HUMAN
395-437
43
2
A:395-437
B:395-437
43
43
1.11
ENST00000325110
11
ENSE00000742603
chr5:
43292739-43292576
164
HMCS1_HUMAN
437-491
55
2
A:437-470
B:437-470
34
34
1.12
ENST00000325110
12
ENSE00001379212
chr5:
43291322-43289497
1826
HMCS1_HUMAN
492-520
29
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_HMG_CoA_synt_C_2p8uB01 (B:187-469)
1b: PFAM_HMG_CoA_synt_C_2p8uB02 (B:187-469)
2a: PFAM_HMG_CoA_synt_N_2p8uB03 (B:16-186)
2b: PFAM_HMG_CoA_synt_N_2p8uB04 (B:16-186)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Thiolase
(72)
Family
:
HMG_CoA_synt_C
(5)
Homo sapiens (Human)
(2)
1a
HMG_CoA_synt_C-2p8uB01
B:187-469
1b
HMG_CoA_synt_C-2p8uB02
B:187-469
Family
:
HMG_CoA_synt_N
(5)
Homo sapiens (Human)
(2)
2a
HMG_CoA_synt_N-2p8uB03
B:16-186
2b
HMG_CoA_synt_N-2p8uB04
B:16-186
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (169 KB)
Header - Asym.Unit
Biol.Unit 1 (162 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2P8U
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help